Hi,

I have an ExpressionSetIllumina object with 12 samples. Is there a 
way to subset on the samples and create a new ExpressionSetIllumina 
object? The description of the ExpressionSetIllumina class has a 
combine() method for two ExpressionSetIllumina objects, and also has this:

object[(index):
Conducts subsetting of matrices and phenoData and reporterInfo components
# shouldn't this read object[(index)]: ?

It appears this subsetting works on the features, not samples:

 > dim(BS.bg.quant)
Features  Samples
    45281       12

 > temp <- BS.bg.quant[1:6]
 > dim(temp)
Features  Samples
        6       12

Trying to subset on samples/columns like you can do for other 
ExpressionSet objects yields this:

 > temp <- BS.bg.quant[,1:6]
Error: subscript out of bounds


Is there a way to subset on samples, or is there a reason why I 
shouldn't subset the object but instead create a new one using 
readBeadSummaryData?

Thanks,
Jenny


Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich@illinois.edu 
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